Neuroscience Grad School: Cliff’s notes

Here’s a quick summary of my life as a scientist in grad school.

Ph.D. in Neuroscience from Baylor College of Medicine
Thesis: Neural Networks and Genetics of Colored Sequence Synesthesia



Left Hemisphere 


Right Hemisphere

How to read these graphs:

Each sphere represents one brain region and is placed in anatomical space.  Blue signifies no significant difference between controls and colored-sequence synesthetes.  Green signifies a significant difference in the way these brain regions cluster together. Clustering in this model describes how nodes fall into modules together, or how they organize into neighborhoods with one another.


While listening to grapheme-rich clips of Sesame Street, colored-sequence synesthetes (who associate color with numbers and letters) cluster visual regions together while controls cluster frontal and parietal regions.  In particular, synesthetes cluster grapheme and color regions more than controls, supporting the suggestion that synesthetes experience color in response to achromatic numbers and letters (graphemes). Tomson et al., In Press.

Is the Kindle actually better for your eyes?

Let’s face it.  We all know someone with the new Amazon Kindle.  On Christmas day 2010, more people activated new Kindles and bought more e-books than at any other time in Amazon’s history.  And why not?  It’s slim, it’s lightweight, and it’s better for your eyes.

Really?  All of my googling yielded a handful of articles claiming that the Kindle is better than the iPad because it’s easier on the eyes, but none addressed the physiological issue of how that could be.  How is it better?  The abundant lack of evidence lead me to do my own research so I could draw a reasonably informed conclusion.  It took more digging than I expected, so rather than waste all that energy on a simple answer, it seemed prudent to share.

Before digging into the answer (skip to the bottom for a basic yes/no), let’s take a moment to review how each technology works.  First, the Kindle.  Kindle screens are created using ‘e-ink’ technology.  Think etch-a-sketch.  Imagine a checkerboard of beach balls.  Each beach ball is filled with ping-pong balls.  For explanation’s sake, let’s simplify further and just take one beach ball full of ping-pong balls.

There are two types of ping-pong balls – black and white.  The black balls carry a positive charge and the white balls carry a negative charge.  The ping-pong balls are just randomly floating around in the beach ball, which is anchored to one square in the checkerboard.  Then BAM.  I hold a negative charge (technically, in the form of an electrode) over the beach ball.  Now, all of the black, positively-charged ping-pong balls are attracted to my new negative charge.  The white ping-pong balls are repelled.  This means that I have a black surface immediately below the place where I apply the negative charge.  THIS means that wherever I apply the negative charge, I get a black beach ball.  So each beach ball effectively becomes a pixel that I can change from black to white simply by applying a positive or negative charge (see image below, adapted from Wikipedia).

The details of how LCD displays work can be found here (, so I won’t go into the minutia.  What’s important to know is that LCD (liquid crystal diode) displays work in a very similar fashion to the e-ink technology I’ve just described.  The difference is that e-ink effectively uses  ambient light.  LCDs, however, do not reflect light.  They require their own light source to be illuminated.  Backlighting is simply a way to provide light to illuminate the various LCDs.  This means you have a wall of LEDs (light emitting diodes) right behind a wall of LCDs (liquid crystal diodes).  LEDs provide the light, LCDs provide the pixellation or pattern of black/white/color.

Here’s what this means for you.  The Kindle only needs to change the pixels.  The iPad and others need to change the pixels AND they need to add light behind so you can see the pixels.  This means that reading an iPad is just like reading a computer screen or watching TV.  Reading on the Kindle is like reading a book.  Books don’t provide the light, you do.  This is why the Kindle is great on the beach – no light source means no glare which means it works well in bright sunlight.  For the same reason, the Kindle is not great if its after bedtime and your spouse is asleep you realize the futility of looking for a flashlight in the dark.

There's no easy diagram for explaining LCD screens, put imagine a matrix of LCDs in different colors (lots of red here) and a wall of LEDs right behind.

So to recap, iPads and other screens use a backlight to illuminate the screen, whereas the Kindle/Nook don’t require it.  The main argument for e-ink, however, is eye strain.  What is eye strain?  It boils down to fatigue brought on by looking at one thing for too long.  Your eyes might get dry, you might find it harder to keep the page in focus, and it might even go as far as to give you a headache.  But you can get eye strain from both devices if you read them for long enough.  One of the major culprits, however, is changing the brightness of the text you are reading.  This requires your pupils to dilate/contract, which takes energy.  Imagine you’re on an iPad reading your book, but then you here the ‘ding!’ that you have a new email.  You quickly switch to your inbox, which leads you to a link, and you browse a bit.  Each web page has different amounts of luminosity (how much light your eye sees), requiring your eyes to do a fair amount of accomodation to the new light levels.  This also contributes to eye strain.  Fortunately (or un- perhaps), this is not a problem for a Kindle that uses only black/white with a set luminance.  You can browse to a webpage, but the luminance stays the same.

In answer to the question of whether the Kindle is actually better for your eyes – I’d say yes, by a slim margin.  Both devices will tire you out if you read for a long time, but the iPad has two downsides in my opinion.  One, if you’re a night reader, this means looking at an illuminated screen when you’re about to sleep which can ultimately keep you awake.  Two, the iPad allows you to browse the web like a computer, and forcing your eye to accomodate to all the different light levels of the various webpages takes its toll.  This is especially the case if you spend all day working at a computer.  So all in all, if you’re in the market for a device that allows you to  just  read books, I’d pick an e-inker.  If you want books and news and email and Angry Birds, clearly the Kindle will not suit your purpose.  But at the end of the day, with all the choices, decisions, and distractions, sometimes it’s nice to come home and pick up a single device for one single purpose.  Then again, you could always skip all this mess and just stick with a good old fashioned book.

Happy reading!

Synesthesia: The Basics

With over 50 forms of synesthesia, this condition represents one of the richest perceptual conditions known to science.  Rather than a deficit, synesthesia describes an augmentation of a very particular sensory experience.  For synesthetes with colored-sequence synesthesia (CSS), the letter ‘K’ is actually ‘K’, Saturday means something very different than just Saturday, and [713] pops into their head right before dialing my hometown area code.  Notice that the color choices are specific.  If you were to ask a synesthete the color of Saturday today and two weeks from today, the answer will be the same.  This is an important feature of synesthesia, as the consistency and specificity of the colors can be used to verify true synesthetic associations.

One critical distinction to make here is that these colors are, in fact, just associations.  I say ‘just’ to emphasize that synesthetes do not mistakenly see this text in different colors.  Rather, the letters trigger an association of color, much like if I were to say Harry Potter, some image would pop into your head as an automatic association with the name.  Nonetheless, you don’t see Harry Potter.  You just have the latest movie trailer stuck in your head until I change the subject.  This is what it is like to be a synesthete, except that you might have these automatic associations between letters and color, between taste and color, between music and shape, or between touch and texture.

What is Synesthesia?

What is synesthesia?

Synesthesia is a perceptual condition where individuals make unusual sensory associations.  There are over 50 different forms of synesthesia, but the most common form is called colored-sequence synesthesia (CSS).  People with CSS associate colors with over-learned sequences including numbers, letters, weekdays, and months.

LMS Color Space

For those of you academics who are utterly befuddled by the confusion that is LMS color space, I offer the following groundwork.  This came about through my own work with synesthesia (see my other posts)  and my latest task: to which areas of the brain care the most about color using functional MRI (fMRI).  Scientific protocol dictates that if you’ve never done something before, pick a lab that has done so and copy it word-for-word.  In the world of color,Brain Wandell‘s lab is the place to be if you want to study anything about how primates process color.  Thusly, I turn to his past works to model a color localizer for fMRI.

Unfortunately, my experience with color up until three days ago included RGB basics and a moderate understanding of rods/cones.  As you  might remember before Home Depot brought a spectrophotometer into the game, matching paint colors was a complete nightmare.  It was easier just to buy 10 times more than necessary than to experience the pain of someday realizing your wall will forever remain chipped.  Actually, there are many different ways we humans have devised to describe color.  Here is a nice little review about how we specify and view color.  [Sidebar – here‘s an interesting article on how children learn color words].  The problem is this – when I ‘see’ a specific shade of green, even that specific shade could be made out of many different color combinations, including various degrees of achromatic (white/black) values.  So if I want to find the areas of the brain that ‘care’ about color, I want to look at brain activity when a person is seeing 100% color vs. 0% color.   Neither RGB nor CIE color space will do the trick, in short because they both describe color perception (i.e. what your brain interprets) rather than color processing (i.e. the signals (wavelengths of light) that your brain receives from the picture or item).  Here’s why:

CIE color space was designed to accurately represent perceptual color judgement.   In other words, regardless of what’s used to make the colors, if they look the same, they’re close in CIE color space.  CIE space was designed for use by manufacturers for easy communication regarding textile colors .  Manufacturers want to know: Does that text look like the same green to me as it does to you?.  It doesn’t matter which combinations of red, green, and blue are used to create it, so long as customers in 50 states agree that the color is perceived as the same color.  This system is unfortunately inconsistent with the physiological basis for color perception.  Physiologically, something has color if the wavelengths of light emanating from the object have different values of Long, Medium, and Short wavelengths.  This is because the human retina has cells (called cones) specifically designed to receive different wavelengths of light.

Enter: LMS color space, representing long, medium, and short light wavelengths (red, green, blue respectively).  This is useful for scientific experiments when you want to control how much certain cells (cones) are excited.  Something else to consider, however, is contrast.  Wandell 2008 found that, no matter the color being shown to the person,some cones (where we expect to find color) respond differently depending on the level of contrast presented to the subject.  This means that in order to localize regions of the brain that care only about color (and not about contrast), it’s important to make sure contrast (luminance) is the same for all of our colorful stimuli.

LMS values range from -1 to 1.  So, black is (-1,-1,-1) and white is (1,1,1), and then there’s everything in between.  MacLeod and Boynton (1979), who invented LMS, defined chromaticity using two dimensions: M+L cone excitation (red-green oppononency) and S cone excitation.  Just like in RGB, if all values are equal, you get gray.  In the literature, gray is described as such: “(L+M)- and S-cone contrast are set equal, and (L-M)-cone contrast is zero”.  The actual values of L,M, and S are all scaled by the sum of L+M, a measure of luminance. To go from gray to a color, all you need to do is change EITHER the S cone OR (L-M).  If L and M are changed by the same amount, they’ll cancel each other out and you get no effect.

That said, the latest and greatest of color localizers is described in Alex Wade and Brian Wandell’s 2008 paper in the Journal of Vision.  Here’s a description of the the stimuli  they used for the chromatic/achromatic simuli.

Achromatic block (12 checkerboards of 12×12 squares, updated every 2 seconds –> a block of 24s length)

The background for all windows is (0,0,0).  Each square subtends 1 degree of visual angle, so the checkerboard subtends 12 degrees on each side.  The range of values that can be selected runs from -1 to 1, for a total range of 2.  Wade varies each square by a randomly-selected +/- 24% of the gray background (0,0,0).  So, 24% of 2 is .48, which means that each square can range anywhere from (-.48,-.48,-.48) to (.48,.48,.48).

For each achromatic checkerboard, a chromatic checkerboard is generated.  The color varies between +/- 6%, which means any value between -.12 and +.12 multiplied by the value of the L cone.  Let’s say I choose 5% (+.1).  If Square 1 in the achromatic checkerboard was selected to be [.24,.24,.24](12% LMS contrast), in the achromatic patch, in the chromatic patch it will be: [.12+.1,.12,.12] (5% (L-M)-contrast).  Voila!  Color.